#for BRCA unnormalized reference creation
 cut -f2 /data4/bsi/bioinf_ext1/s113759/BRCA/RNASEQ2/GENEXP/unc.edu__IlluminaHiSeq_RNASeqV2__TCGA-HN-A2NL-01A-11R-A18M-07__expression_rsem_gene.txt|cut -d '|' -f 2 > reference
#for BRCA unnormalized file creation 
ls /data4/bsi/bioinf_ext1/s113759/BRCA/RNASEQ2/GENEXP/*expression_rsem_gene.txt >file

#for BRCA normalized reference creation
cut -f2 /data4/bsi/bioinf_ext1/s113759/BRCA/RNASEQ2/GENEXP/unc.edu__IlluminaHiSeq_RNASeqV2__TCGA-HN-A2NL-01A-11R-A18M-07__expression_rsem_gene_normalized.txt|cut -d '|' -f 2 > reference

#for BRCA normalized file creation
ls /data4/bsi/bioinf_ext1/s113759/BRCA/RNASEQ2/GENEXP/*expression_rsem_gene_normalized.txt >file
